Implement Python-based CLI

.github/CONTRIBUTING.md

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+# Contributing to LOGAN
+
+TODO -- describe gitflow, require PRs...
+
+## Use pre-commit hooks
+
+Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.
+
+Install [pre-commit](https://pre-commit.com/#installation) if you haven't already,
+then run `pre-commit install` to install the hooks specified in `.pre-commit-config.yaml`.
+Pre-commit will run the hooks every time you commit.
+
+If you re-clone the repo, you will likely need to re-run `pre-commit install`
+as the hooks are installed to the local repo's `.git/hooks` directory.
+
+## Versions
+
+Increment the version number following semantic versioning[^1] in the `VERSION` file.
+
+[^1]: semantic versioning guidelines https://semver.org/
+
+## Changelog
+
+Keep the changelog up to date with all notable changes in `CHANGELOG.md`[^2].
+
+[^2]: changelog guidelines: https://keepachangelog.com/en/1.1.0/
+
+## VS code extensions
+
+If you use VS code, installing [nf-core extension pack](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) is recommended.

.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [pipeline documentation: troubleshooting](https://ccbr.github.io/LOGAN/user-guide/troubleshooting/)
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop any relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+        If the bug is related to a GUI, add screenshots to help explain your problem.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity)_
+        * OS _(eg. Ubuntu Linux, macOS)_
+        * Version of CCBR/TOOL_NAME _(eg. 1.0, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

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+contact_links:
+  - name: Discussions
+    url: https://github.com/CCBR/LOGAN/discussions
+    about: Please ask and answer questions here.

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Suggest an idea for the pipeline
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/PULL_REQUEST_TEMPLATE.md

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+## Changes
+
+<!--
+Provide a summary of what is included in this Pull Request (PR).
+-->
+
+## Issues
+
+<!--
+Reference any issues related to this PR.
+If this PR fixes any issues, [use a keyword](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword)
+when referring to the issue.
+-->
+
+<!--
+**Reviewers**: Use the @ feature to mention anyone responsible for reviewing/completing this request.
+-->
+
+## PR Checklist
+
+(~Strikethrough~ any points that are not applicable.)
+
+- [ ] This comment contains a description of changes with justifications, with any relevant issues linked.
+- ~[ ] Write unit tests for any new features, bug fixes, or other code changes.~ _testing framework not yet implemented_
+- [ ] Update docs if there are any API changes.
+- [ ] If a new nextflow process is implemented, define the process `container` and `stub`.
+- [ ] Update `CHANGELOG.md` with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

.github/workflows/build.yml

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+name: build
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - main
+      - develop
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install nextflow
+        uses: nf-core/setup-nextflow@v1
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install .[dev,test]
+          python -c 'from logan.src.util import chmod_bins_exec; chmod_bins_exec()'
+      - name: Test stub run
+        run: |
+          mkdir tmp && cd tmp
+          which logan
+          logan init
+          logan run -profile ci_stub,docker -stub

.github/workflows/docs.yml

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+name: mkdocs_build
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+
+env:
+  actor: "41898282+github-actions[bot]"
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: git config
+        run: |
+          git config --local user.email "${actor}@users.noreply.github.com"
+          git config --local user.name "$actor"
+      - run: pip install --upgrade pip
+      - run: pip install -r docs/requirements.txt
+      - run: mkdocs gh-deploy --force

.github/workflows/projects.yml

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+name: Add issues/PRs to user projects
+
+on:
+  issues:
+    types:
+      - assigned
+  pull_request:
+    types:
+      - assigned
+
+jobs:
+  add-to-project:
+    uses: CCBR/.github/.github/workflows/[email protected]
+    secrets: inherit

.gitignore

@@ -1 +1,55 @@
 docs/user-guide/site/
+
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+replay_pid*
+
+# nextflow
+.nextflow*
+/work*/
+/data/
+/results/
+/output/
+/params.yaml
+
+# python packaging
+*.pyc
+*.egg-info
+/build
+
+# macOS
+.DS_Store
+
+# code editors
+.vscode/
+*.code-workspace
+
+# user-specific dev files
+*KLS*
+*.Rproj
+.Rproj.user
+.Rhistory
+
+/submit_slurm.sh
+/tmp/

CHANGELOG.md

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+# LOGAN development version
+
+- Python-based CLI

VERSION

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+0.1.0-dev

assets/slurm_header_biowulf.sh

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+#!/usr/bin/env bash
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=1g
+#SBATCH --time=1-00:00:00
+#SBATCH --parsable
+#SBATCH -J "tool_name"
+#SBATCH --mail-type=BEGIN,END,FAIL
+#SBATCH --output "log/slurm_%j.log"
+#SBATCH --output "log/slurm_%j.log"
+
+module load ccbrpipeliner
+module load nextflow
+NXF_SINGULARITY_CACHEDIR=/data/CCBR_Pipeliner/SIFS

assets/slurm_header_frce.sh

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+#!/usr/bin/env bash
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=1g
+#SBATCH --time=1-00:00:00
+#SBATCH --parsable
+#SBATCH -J "tool_name"
+#SBATCH --mail-type=BEGIN,END,FAIL
+#SBATCH --output "log/slurm_%j.log"
+#SBATCH --output "log/slurm_%j.log"
+
+module load nextflow
+NXF_SINGULARITY_CACHEDIR=/mnt/projects/CCBR-Pipelines/SIFs

conf/base.config

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+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow base config file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    A 'blank slate' config file, appropriate for general use on most high performance
+    compute environments. Assumes that all software is installed and available on
+    the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 2
+    maxErrors     = '-1'
+
+    // Process-specific resource requirements
+    // NOTE - Please try and re-use the labels below as much as possible.
+    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
+    //        If possible, it would be nice to keep the same label naming convention when
+    //        adding in your local modules too.
+    // TODO nf-core: Customise requirements for specific processes.
+    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+    withLabel:process_single {
+        cpus   = { check_max( 1                  , 'cpus'    ) }
+        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_low {
+        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_medium {
+        cpus   = { check_max( 16    * task.attempt, 'cpus'    ) }
+        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high {
+        cpus   = { check_max( 32     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 120.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 16.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_long {
+        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high_memory {
+        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+    }
+    withLabel:error_ignore {
+        errorStrategy = 'ignore'
+    }
+    withLabel:error_retry {
+        errorStrategy = 'retry'
+        maxRetries    = 2
+    }
+}